Merge NAST and Infernal alignments

Purpose

This tool merges sequence alignments from NAST and Infernal into one alignment file. The merge process works by replacing the long unaligned portions of the Infernal alignment with the corresponding region from the NAST alignment.

The threshold setting is used to determine which sections of the alignments are going to be replaces. It corresponds to the minimum width of such a section.

Since both Infernal and NAST may remove sequences from the alignment using various criteria, the alignment returned by this tool contains the sequences present in both files.

This tool takes as input a FASTA-formatted alignment file from NAST (or a zip file containing this alignment), a FASTA-formatted alignment file from RDP/Infernal coming from the same sequences (or a zip file containing this alignment), and the threshold for searching unaligned sections. The tool returns a FASTA-formatted alignment file.